The purpose of this study is to develop a new approach in modeling and simulation of a reverse osmosis desalination system by using fractional differential equations. Using the Legendre wavelet method combined with the decoupling and quasi-linearization technique, we demonstrate the validity and applicability of our model. Examples are developed to illustrate the fractional differential technique and to highlight the broad applicability and the efficiency of this method. The fractional derivative is described in the Caputo sense.